#include <yat/utility/SmithWaterman.h>

Public Member Functions
	SmithWaterman (double gap=0, double open_gap=0)
	Constructor. More...

	SmithWaterman (double vertical_gap, double open_vertical_gap, double horizon_gap, double open_horizon_gap)
	Constructor. More...

const Aligner::Cigar &	cigar (void) const

size_t	position (void) const

const Matrix &	score (void) const

double	operator() (const MatrixBase &dot)

template<typename RandomAccessIterator1 , typename RandomAccessIterator2 >
double	operator() (RandomAccessIterator1 reference_begin, RandomAccessIterator1 reference_end, RandomAccessIterator2 query_begin, RandomAccessIterator2 query_end, double mismatch=0)

Detailed Description

Since: New in yat 0.12

Constructor & Destructor Documentation

◆ SmithWaterman() [1/2]

theplu::yat::utility::SmithWaterman::SmithWaterman	(	double	gap = `0`,
		double	open_gap = `0`
	)

explicit

Constructor.

Same as SmithWaterman(gap, open_gap, gap, open_gap)

◆ SmithWaterman() [2/2]

theplu::yat::utility::SmithWaterman::SmithWaterman	(	double	vertical_gap,
		double	open_vertical_gap,
		double	horizon_gap,
		double	open_horizon_gap
	)

Constructor.

Parameters

vertical_gap	Penalty for extending a vertical gap. A vertical gap means consuming a reference element i.e. a deletion in query sequence.
open_vertical_gap	Open a deletion. Total cost for a deletion is open_vertical_gap + N * vertical_gap.
horizon_gap	Penalty for extending a insertion.
open_horizon_gap	Penalty for open an insertion. Total penalty for a insertion is open_horizon_gap + N * horizon_gap.

Member Function Documentation

◆ cigar()

const Aligner::Cigar& theplu::yat::utility::SmithWaterman::cigar ( void ) const

The CIGAR here is slightly different compared to CIGAR in Aligner as it uses BAM_CEQUAL and BAM_CDIFF rather than BAM_CMATCH, and it also uses BAM_CSOFT_CLIP and ends of CIGAR to reflect if whole query was aligned.

Returns: CIGAR reflecting latest performed alignment

◆ operator()() [1/2]

double theplu::yat::utility::SmithWaterman::operator() ( const MatrixBase & dot )

Find best alignment using Smith-Waterman algorithm based on the dot-matrix. Each row in dot corresponds to an element in reference, and each column corresponds to an element in the query.

Returns: smith-waterman score

◆ operator()() [2/2]

template<typename RandomAccessIterator1 , typename RandomAccessIterator2 >

double theplu::yat::utility::SmithWaterman::operator()	(	RandomAccessIterator1	reference_begin,
		RandomAccessIterator1	reference_end,
		RandomAccessIterator2	query_begin,
		RandomAccessIterator2	query_end,
		double	mismatch = `0`
	)

Calculate a dot-matrix of size query_end-query_begin X reference_end-reference_begin where the element ij is 1.0 if reference_begin[i] == query_begin[j] and -mismatch otherwise.

Type Requirements:

RandomAccessIterator1 is a Readable Iterator
RandomAccessIterator1 is a Random Access Traversal Iterator
RandomAccessIterator2 is a Readable Iterator
RandomAccessIterator2 is a Random Access Traversal Iterator

◆ position()

size_t theplu::yat::utility::SmithWaterman::position ( void ) const

Returns: position i.e. first element in reference that is aligned to the query.

◆ score()

const Matrix& theplu::yat::utility::SmithWaterman::score ( void ) const

Returns: score matrix

The documentation for this class was generated from the following file:

yat/utility/SmithWaterman.h

Public Member Functions